+Open data
-Basic information
Entry | Database: PDB / ID: 4asc | ||||||
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Title | Crystal structure of the Kelch domain of human KBTBD5 | ||||||
Components | KELCH REPEAT AND BTB DOMAIN-CONTAINING PROTEIN 5 | ||||||
Keywords | PROTEIN BINDING / CYTOSKELETON / KELCH REPEAT | ||||||
Function / homology | Function and homology information skeletal muscle fiber differentiation / I band / A band / Cul3-RING ubiquitin ligase complex / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / skeletal muscle fiber development / negative regulation of protein ubiquitination / positive regulation of protein ubiquitination / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Canning, P. / Ayinampudi, V. / Krojer, T. / Strain-Damerell, C. / Raynor, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural Basis for Cul3 Assembly with the Btb-Kelch Family of E3 Ubiquitin Ligases. Authors: Canning, P. / Cooper, C.D.O. / Krojer, T. / Murray, J.W. / Pike, A.C.W. / Chaikuad, A. / Keates, T. / Thangaratnarajah, C. / Hojzan, V. / Marsden, B.D. / Gileadi, O. / Knapp, S. / von Delft, F. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4asc.cif.gz | 136.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4asc.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 4asc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/4asc ftp://data.pdbj.org/pub/pdb/validation_reports/as/4asc | HTTPS FTP |
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-Related structure data
Related structure data | 2vpjC 2xn4C 3ii7C 4ap2C 4apfC 2wozS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35252.977 Da / Num. of mol.: 1 / Fragment: KELCH DOMAIN, RESIDUES 314-616 Source method: isolated from a genetically manipulated source Details: CYS 340 WAS OXIDISED IN THE CRYSTAL STRUCTURE. / Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q2TBA0 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | SER 345 TO ASN IS DOCUMENTED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.31 % / Description: NONE |
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Crystal grow | Details: 0.1 M CITRATE PH 5.3, 20%(W/V) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→39.89 Å / Num. obs: 34642 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 18.12 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.78→1.82 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WOZ Resolution: 1.78→52.51 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.218 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.116 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→52.51 Å
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Refine LS restraints |
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